Installation¶
Table of Contents¶
Environment Setup¶
Dependencies:¶
- Nextflow v. 21.10.3 or newer
- Compute environment (docker, singularity or conda)
❗ Note: If you are a CDC user, please follow the set-up instructions found on this page: CDC User Guide
(1) Clone the repository to your local machine:¶
git clone https://github.com/CDCgov/tostadas.git
❗ Note: If you already have Nextflow installed in your local environment, skip ahead to step 5.
(2) Install mamba and add it to your PATH¶
2a. Install mamba
❗ Note: If you have mamba installed in your local environment, skip ahead to step 3.
curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge
2b. Add mamba to PATH:
export PATH="$HOME/mambaforge/bin:$PATH"
(3) Install Nextflow using mamba and the bioconda Channel¶
mamba install -c bioconda nextflow
Run a test submission¶
(1) Update the default submissions config file with your NCBI username and password¶
# update this config file (you don't have to use vim)
vim conf/submission_config.yaml
(2) Run the workflow with default parameters and the local run environment¶
# test command for virus reads
nextflow run main.nf -profile mpox,test,<singularity|docker|conda> --workflow biosample_and_sra
The pipeline outputs appear in tostadas/results
Start submitting your own data¶
Create an NCBI Center Account. See NCBI Center Account
Choose a workflow and specify your profile or (optionally, for annotation and GenBank submission) an organism_Type and virus_subtype. See: Putting together the Nextflow command
Please read the Submission Guide for important details about parameters you need to specify. Please especially note the following:
* prod_submission: true/false (for submitting to Test vs. Production server). See Other customizations
* batch_size: for submitting large datasets in chunks. We highly recommend you submit using batches! See Other customizations
* workflow: read how to use TOSTADAS for different types of submissions. See Submitting to Production
* profiles: read about profile shortcuts in Using specific profiles